Convert Ensembl IDs to gene symbols.

Convert Ensembl IDs to gene symbols.

ens2sym(x, orgdb, BMdataset = "")

Arguments

x

A BbcSE object.
orgdb

A OrgDb object. Download the annotations for your species from 'http://bioconductor.org/packages/release/BiocViews.html#___OrgDb'. Only used if BMdataset="".
BMdataset

character. The name of the BM dataset you want to use. Try to use 'bbcRNA::searchBM("species_name")' to find the appropriate dataset if needed.

Value

A BbcSE object.

Details

Gene symbols with more than one Ensembl ID match are determined only from genes present in the BbcSE object, so be sure it is unfiltered.

  • Symbols that match multiple Ensembl IDs will be resolved by concatenating the Ensembl ID and the gene symbol. Uses scater::uniquifyFeatureNames.

  • Genes with multiple possible symbols will be labelled as Ensembl ID.

  • Genes absent from OrgDb/Biomart will be labelled as Ensembl ID.